Solution Phase Combinatorial Chemistry. Purine- and Pyrimidine-Based Libraries with Antibacterial Activity via Solution Phase Simultaneous Addition of Functionalities

Abstract

We have effectively used the SPSAF method with purine and pyrimidine based scaffolds to rapidly generate diverse libraries with antibacterial activity. Deconvolution via HPLC fractionation resulted in libraries with reduced complexity (2–10 compounds), a number of which retained good antibacterial activity.     

MCR III1. Multicomponent Reactions and Their Libraries,a New Type of Organic Chemistry of the Isocyanides and Phosphorus Derivatives.

Abstract

Various new one-pot multicomponent reactions (MCRs) of C^II and P^III derivatives and their libraries are described here. The preparation of some nucleobase- and phospholipid compound libraries by MCRs have been carried out.

     

Purine Based Combinatorial Chemistry: Solution Phase Simultaneous Addition of Functionalities. Iterative Deconvolution by Orthogonal Protection to a Single Compound with Potent Antibacterial Activity

Abstract

We have recently described a method to prepare combinatorial chemistry libraries by solution phase simultaneous addition of functionalities (SPSAF).^1–2 SPSAF has been used to create libraries based on the purine heterocycle. The nucleophilic sites (secondary nitrogens) in the planer heteroaromatic purine scaffold were built in via linkers. Thus, to continue the use of electophilic functionalities, as in previous libraries, a bifunctional nucleophilic linker was required. Piperazines readily served this purpose. Nucleophilic displacement of the chloro groups on 2,6-dichloropurine with piperazines provides reactive, constrained secondary amines for combinatorialization (Figure 1, 1). An additional piperazine was placed in the 9-position by alkylation of 2,6-dipiperazinylpurine. In this manner, the functionality that differentiates each pool (sublibrary) could be placed last in the synthetic scheme (fix last concept).¹     

Digital analysis of cDNA abundance; expression profiling by means of restriction fragment fingerprinting

Background  

Gene expression profiling among different tissues is of paramount interest in various areas of biomedical research. We have developed a novel method (DADA, Digital Analysis of cDNA Abundance), that calculates the relative abundance of genes in cDNA libraries.     

A Rapid Method for the Preparation of a One Dimensional Sequence-Overlapping Oligonucleotide Library

Abstract

A new synthesis modul was constructed to prepare one-dimensional libraries of sequentally overlapping oligonucleotides on surface modified polypropylene tapes. The use of such a library for the diagnostic screening of a point mutation in the regulatory protein gene p53 is described.     

Improved Synthesis of Trinucleotide Phosphoramidites and Generation of Randomized Oligonucleotide Libraries

A new method to produce a set of 20 high quality trinucleotide phosphoramidites on a 5–10 g scale each was developed. The procedure starts with condensation reactions of P-components with N-acyl nucleosides, bearing the 3 ′-hydroxyl function protected with 2-azidomethylbenzoyl, to give fully protected dinucleoside phosphates 13. Upon cleavage of dimethoxytrityl group from 13, dinucleoside phosphates 16 are initially transformed into trinucleoside diphosphates 19 and then the 2-azidomethylbenzoyl is selectively removed under neutral conditions to generate trinucleoside diphosphates 5 in excellent yield. Subsequent 3 ′-phosphitylation affords target trinucleotide phosphoramidites 7. When mutagenic oligonucleotides are synthesized employing mixtures of building blocks 7 as well as following the new synthetic protocol, representative oligonucleotide libraries are generated in good yields.     

Microwave assisted,one-pot synthesis of 5-nitro- 2-aryl substituted-1H-benzimidazole libraries: Screening in vitro for antimicrobial activity

The efficient and rapid synthesis of 5-nitro-2-aryl substituted-1H-benzimidazole libraries (1a-1j) has been established. Thus, both microwave and conventional cyclo-condensation of 4-nitro ortho-phenylenediamine with various phenoxyacetic acids were carried out in the presence of HCl catalyst. The microwave synthesis route afforded advantages, such as good to excellent yields, shorter reaction time (2.5–3.5?min), readily available starting material, and simple purification procedure, which distinguish the present protocol from other existing methods used for the synthesis of benzimidazole libraries. Bioassay indicated that all the compounds showed in vitro antimicrobial activity against Vancomycin resistant enteroccoccus, Staphylococcus aureus, Micrococcus, Bacillus subtilis (gram-positive bacteria) and Shigella dysentery, Escherichia coli (gram-negative bacteria) and Candida albicans, Aspergillus niger, Penicillium (fungi). The minimum inhibitory concentration (MIC) was determined for test compounds as well as for reference standards.     

Exploration of Natural and Artificial Sequence Spaces: Towards a Functional Remodeling of Membrane-bound Cytochrome P450

Abstract

Two complementary methods are described that associate in vitro and in vivo steps to generate sequence diversity by segment directed saturated mutagenesis and family shuffling. A high-throughput DNA chip-based procedure for the characterization and potentially the equalization of combinatorial libraries is also presented. Using these approaches, two combinatorial libraries of cytochrome P450 variants derived from the CYP1A subfamily were constructed and their sequence diversity characterized. The results of functional screening using high-throughput tools for the characterization of membrane P450-catalyzed activities, suggest that the 204–214 sequence segment of human CYP1A1 is not critical for polycyclic aromatic hydrocarbon recognition, as was hypothesized from previous data. Moreover, mutations in this segment do not alter the discrimination between alkoxyresorufins, which, for all tested mutants, remained similar to that of wild-type CYP1A1. In contrast, the constructed CYP1A1–CYP1A2 mosaic structures, containing multiple crossovers, exhibit a wide range of substrate preference and regioselectivity. These mosaic structures also discriminate between closely related alkoxyresorufin substrates. These results open the way to global high-throughput analysis of structure–function relationships using combinatorial libraries of enzymes together with libraries of structurally related substrates.     

东太平洋多金属结核区两个站位深海沉积物细菌多样性北大核心CSCD

【目的】为了解东太平洋中国多金属结核勘探合同区西区2个站位(WBC1305和WBC1316A)深海沉积物细菌群多样性。【方法】直接提取环境样品总基因组,通过PCR和TA克隆策略构建了2个站位6个层次16S r RNA基因文库,对2个站位沉积物表层泥样中细菌多样性和群落结构特征进行分析,并通过构建系统发育树,进行系统发育学分析。【结果】2个站位6个文库共获得有效克隆533个,其中472个克隆包括α-变形菌纲、β-变形菌纲、γ-变形菌纲、δ-变形菌纲、浮霉菌门、酸杆菌门、硝化螺旋菌门、放线菌门、绿弯菌门、厚壁菌门、拟杆菌门、迷踪菌门、芽单胞菌门、Hydrogenedentes、Chlorobi和Nitrospinae16个细菌类群,而另外61个克隆为不可分类细菌类群。【结论】结果表明γ-变形菌纲和厚壁菌门分别是WBC1305和WBC1316A站位的优势种群;WBC1316A站位细菌群落结构更加丰富和复杂。     

An efficient method for mutant library creation in Pichia pastoris useful in directed evolution

Abstract

The yeast Pichia pastoris is being increasingly used as a host for expressing enzymes on a large scale, but application in directed evolution requiring efficient expression of libraries of mutants is hampered due to the time-consuming multistep procedure which includes an intermediate bacterial host (Escherichia coli). Here we introduce a fast and highly simplified method to produce gene libraries in P. pastoris expression vectors. For the purpose of illustration, Galactomyces geotrichum lipase 1 (GGL1) was used as the catalyst in the enantioselective hydrolytic kinetic resolution of 2-methyldecanoic acid p-nitrophenyl ester, the gene mutagenesis method being saturation mutagenesis. The phosphorylated linear plasmid which is integrated in the yeast genome was obtained by combination of partially overlapped fragments using overlap-extension PCR. An intermediate bacterial host is not necessary, neither are restriction enzymes. This method is also applicable when using error-prone PCR for library creation in directed evolution.     

Synthesis of Polyaminooligonucleotides and Their Combinatorial Libraries

Abstract

A synthesis of phosphoramidites of 2′-deoxyadenosine and 2′-deoxyguanosine carrying a protected spermine moiety at N-6 and N-2 positions respectively is described. An approach to analyse properties of polyaminooligonucleotides using their synthetic combinatorial libraries is described and discussed. A synthesis of a polyaminooligonucleotide combinatorial library was carried out and the analysis of the library clearly showed that the presence of spermine moieties in oligodeoxyribonucleotides increases stability of their complexes.     

Mini-review: Combinatorial approaches for the design of novel coating systems

Abstract

Combinatorial and high throughput experimental methods are being applied to the design and development of novel polymers and coatings used in a number of application areas. Methods have been developed for polymer synthesis and screening and for the development of polymer thin film and coating libraries and the screening of these libraries for key properties such as surface energy and modulus. Combinatorial and high throughput methods enable the efficient exploration of a large number of compositional variables over a wide range. In the development of coatings for use in the marine environment, the key challenge is in the development of screening methods that can predict good performance. A number of assays are under development that will permit the rapid screening of the interaction of coatings with representative marine organisms.     

Solid-phase Parallel Synthesis of 4-β-D-Ribofuranosylpyrazolo[4,3-d]pyrimidine Nucleosides

The synthesis of pyrazolo[4,3-d]pyrimidine nucleoside library using solid-phase parallel synthesis methodology is described. Glycosylation of the trimethylsilyl (TMS) derivative of 1- and 2-(methyl)-1H and 2H-pyrazolo[4,3-d]pyrimidine-5,7-(4H,6H)-dione (5) with 1-O-acetyl-2,3,5-tri-O-benzoyl-D-ribofuranose in the presence of TMS triflate provided two novel protected nucleosides 6 and 7. The structures of 6 and 7 were assigned by 1H and 2D NMR experiments. Nucleosides 6 and 7 were then transformed to the key intermediates 12 and 15 respectively. Reaction of 12 and 15 with MMTCl resin in the presence of 2,6-lutidine afforded the necessary scaffolds B and C. Different amines (96) were introduced selectively by nucleophilic substitution on scaffolds B and C using solid-phase parallel semi-automated synthesizer. Cleavage of the products from the solid support with 30% HFIP in a parallel fashion yielded nucleoside libraries simultaneously, and they were analyzed and characterized by high-throughput LC-MS.     

Screening of cDNA Libraries with Oligonucleotides as Applied to Signal Transducing G Proteins,Receptors and Effectors

Abstract

Screening of cDNA libraries constructed in phage or plasmids with oligonucleotide probes has become one of the preferred cloning techniques with the least number of false positive failures. In this article we present our current protocols for designing the procedure to detect cDNA inserts and isolate them. We illustrate with primary screens for G protein subunits and membrane receptors.     

Genome-wide identification of conserved microRNA and their response to drought stress in Dongxiang wild rice (Oryza rufipogon Griff.)

Objectives

To identify drought stress-responsive conserved microRNA (miRNA) from Dongxiang wild rice (Oryza rufipogon Griff., DXWR) on a genome-wide scale, high-throughput sequencing technology was used to sequence libraries of DXWR samples, treated with and without drought stress.

Results

505 conserved miRNAs corresponding to 215 families were identified. 17 were significantly down-regulated and 16 were up-regulated under drought stress. Stem-loop qRT-PCR revealed the same expression patterns as high-throughput sequencing, suggesting the accuracy of the sequencing result was high. Potential target genes of the drought-responsive miRNA were predicted to be involved in diverse biological processes. Furthermore, 16 miRNA families were first identified to be involved in drought stress response from plants.

Conclusion

These results present a comprehensive view of the conserved miRNA and their expression patterns under drought stress for DXWR, which will provide valuable information and sequence resources for future basis studies.

     

A Dodecapeptide Selected by Phage Display as a Potential Theranostic Probe for Colon Cancers

AimColon cancer is one of the leading causes of cancer-related mortality. However, specific biomarkers for its diagnosis or treatment are not established well.MethodsWe developed a colon-cancer specific peptide probe using phage display libraries. We validated the specificity of this probe to colon cancer cells with immunohistochemical staining and FACS analysis using one normal cell and five colon cancer cell lines.ResultsThis peptide probe maintained binding affinity even after serum incubation. For therapeutic applications, this peptide probe was conjugated to hematoporphyrin, a photosensitizer, which showed a significantly enhanced cellular uptake and high photodynamic effect to kill tumor cells. As another application, we made a nanoparticle modified from the peptide probe. It efficiently delivered SN-38, an anticancer drug, into tumor cells, and its tumor-targeting ability was observed in vivo after intravenous injection to the same xenograft model.ConclusionThe noble dodecapeptide probe can be a promising candidate for both colon tumor diagnosis and targeted drug delivery.     

A Resource Guide to Travel Film Repositories

Travel films, broadly defined, exist in most moving image collections. Theatrical shorts and features, television series, tourism promotion films, professional and amateur lecture films, expeditionary films and footage, unedited amateur footage are all held by regional and government archives, museums, historical societies, universities, libraries, commercial footage houses, and film distributors. The following is intended to be an annotated guide to a representative set of repositories in North America containing significant amounts of travel film material.     

Large-Scale Solid-Phase Preparation of 3′-Unprotected Trinucleotide Phosphotriesters - Precursors for Synthesis of Trinucleotide Phosphoramidites

Abstract

The approach to large-scale solid-phase synthesis of 3′-unprotected trinucleotide phosphotriesters has been developed. The trinucleotides have been synthesized in 5 g scale by phosphotriester approach using CPG with pore size 70A. Total yield of target products was 75–90%. The molar extinctions of trinucleotides at various wavelengths were calculated; the experimental UV-spectra of trinucleotides show a good agreement with theoretical ones. The trinucleotides synthesized were used for synthesis of trinucleotide phosphoramidites - synthons for generation of DNA/peptide libraries.